In planta transcriptome analysis of Pseudomonas syringae pv. tomato DC3000 during early infection and early exposure to pattern-triggered immunity in Arabidopsis thaliana

We develop a protocol for extracting P. syringae transcriptome from infected A. thaliana tissue through physical separation by low speed centrifugation. We use this protocol to compare the RNASeq transcriptome profiles of DC3000 during naïve host infection and exposure to pattern triggered immunity at 1, 3, and 5 hours post inoculation Bacteria extracted from naïve mock-treated leaves at 1, 3, and 5 hours post inoculation. Bacteria extracted from immune-induced leaves at 1, 3, and 5 hours post inoculation. Bacterial initial inoculum as in vitro media-based sample. Samples collected in triplicate on different days for each time and treatment